Data standardization implementation and applications within and among diagnostic laboratories: integrating and monitoring enteric coronaviruses

Abstract

Every day, thousands of samples from diverse populations of animals are submitted to veterinary diagnostic laboratories (VDLs) for testing. Each VDL has its own laboratory information management system (LIMS), with processes and procedures to capture submission information, perform laboratory tests, define the boundaries of test results (i.e., positive or negative), and report results, in addition to internal business and accounting applications. Enormous quantities of data are accumulated and stored within VDL LIMSs. There is a need for platforms that allow VDLs to exchange and share portions of laboratory data using standardized, reliable, and sustainable information technology processes. Here we report concepts and applications for standardization and aggregation of data from swine submissions to multiple VDLs to detect and monitor porcine enteric coronaviruses by RT-PCR. Oral fluids, feces, and fecal swabs were the specimens submitted most frequently for enteric coronavirus testing. Statistical algorithms were used successfully to scan and monitor the overall and state-specific percentage of positive submissions. Major findings revealed a consistently recurrent seasonal pattern, with the highest percentage of positive submissions detected during December-February for porcine epidemic diarrhea virus, porcine deltacoronavirus, and transmissible gastroenteritis virus (TGEV). After 2014, very few submissions tested positive for TGEV. Monitoring VDL data proactively has the potential to signal and alert stakeholders early of significant changes from expected detection. We demonstrate the importance of, and applications for, data organized and aggregated by using LOINC and SNOMED CTs, as well as the use of customized messaging to allow inter-VDL exchange of information.

Keywords: PDCoV; PEDV; TGEV; data integration; data standardization; enteric coronavirus; monitoring; veterinary diagnostic laboratories.

Figure 1.

Number of submissions tested for A. porcine epidemic diarrhea virus (PEDV), B. porcine deltacoronavirus (PDCoV), C. transmissible gastroenteritis virus (TGEV), and percent of positive results over time. Column charts present the number of tested submissions on the left y-axis, and the lines present the percent of submissions with a RT-PCR–positive result on the right y-axis. The seasons are organized by seasons: winter (Wi) = December–February; spring (Sp) = March–May; summer (Su) = June–August; fall (Fa) = September–November. For the Swine Disease Reporting System (SDRS) database, a full 4-season cycle starts 1 December and ends 30 November of the subsequent year.

Figure 2.

Proportions of specimen types according to number of cases submitted for testing by RT-PCR over time. A. Porcine epidemic diarrhea virus (PEDV). B. Porcine deltacoronavirus (PDCoV). C. Transmissible gastroenteritis virus (TGEV). Each bar represents a year starting on 1 December and ending 30 November of the subsequent year. Each color within a bar represents a different specimen or age category. Only values ≥5% are written in the charts.

Figure 3.

Proportions of submissions by age category according to the number of cases submitted for testing by RT-PCR over time. A. Porcine epidemic diarrhea virus (PEDV). B. Porcine deltacoronavirus (PDCoV). C. Transmissible gastroenteritis virus (TGEV). Each bar represents a year starting on 1 December and ending 30 November of the subsequent year. Each color within a bar represents a different specimen or age category. Only values ≥5% are written in the charts.

Figure 4.

Monitoring enteric coronavirus percentage of positive submissions obtained by testing samples with RT-PCR testing. A. Porcine epidemic diarrhea virus (PEDV). B. Porcine deltacoronavirus (PDCoV). C. Transmissible gastroenteritis virus (TGEV). x-axis: year and week; y-axis: percent of positive submissions. Continuous blue line: predicted weekly percentage of positive results; continuous red line: observed percentage of weekly positive submissions. Blue band: 95% CI for the weekly predicted percentage of positive results for the upcoming year.

Figure 5.

Porcine epidemic diarrhea virus (PEDV) and porcine deltaconavirus (PDCoV) state-level monitoring for January–May 2020. Each color-filled state represents the changes in SD from the predicted state-specific percentage of positive submissions baseline. Baselines were state-specific and constructed using at least 3 y of monthly historical results.